Any of the attractions included on the City Pass are great for kids
http://www.citypass.com/san-francisco
Definitely choose the Exploratorium over the De Young Museum, and the Monterey Bay Aquarium over the Aquarium of the Bay

You also have the option to substitute Alcatraz over the bay cruise which is what we did, but my son was 13 months at the time and happy to just get carried around in the Ergo. Not sure how much he would enjoy it now (almost 3)

We went down there again last month, and this time my son really enjoyed riding around on public transportation (cable cars, street cars, BART, etc), he liked the San Francisco zoo (great zoo, and even better play structure), and he LOVED Happy Hollow Park & Zoo in San Jose. We also had a great time checking out parks and playgrounds this trip. Two faves were the Mission Delores Park, and the Sue Bierman Park Playground (we stay at the Hyatt Regency and this is literally right next door)